Sample name: H9_treated_PRO-seq_2

Log file Pipeline profile Pipeline commands Stats summary file


Looper stats summary

sample_name H9_treated_PRO-seq_2
sample_desc H9 treated PRO-seq
treatment 200 nM romidepsin
replicate 2
toggle 1
protocol PRO
organism human
read_type PAIRED
cell_type H9
purpose high pause index; differential analysis
umi_status true_8
umi_length 8
data_source SRA
read1 /project/shefflab/data/guertin/fastq/H9_200nM_romidepsin_...
read2 /project/shefflab/data/guertin/fastq/H9_200nM_romidepsin_...
srr H9_200nM_romidepsin_rep2
Sample_title H9_200nM_romidepsin_rep2
Sample_geo_accession GSM4214084
Sample_source_name_ch1 H9 cells
File_mb 2737.32
Read_type paired
Genome hg38
Raw_reads 114083518
Fastq_reads 114083518
Reads_with_adapter 43984199.0
Uninformative_adapter_reads 27614116.0
Duplicate_reads 2388789.0
Pct_uninformative_adapter_reads 48.4104
Trimmed_reads 57348074
Trim_loss_rate 49.73
Peak_adapter_insertion_size 20
Degradation_ratio 1.0037
Aligned_reads_human_rDNA 5458620.0
Alignment_rate_human_rDNA 9.52
Mapped_reads 44741250
QC_filtered_reads 25860518
Aligned_reads 18880731.5
Alignment_rate 32.92
Total_efficiency 16.55
Read_depth 3.37
Mitochondrial_reads 670904
Maximum_read_length 38
Genome_size 3099922541
Frac_exp_unique_at_10M 0.8186
NRF 1.0
PBC1 10123508.0
PBC2 10123508.0
Unmapped_reads 6731776
TSS_coding_score 57.4
TSS_non-coding_score 16.5
Pause_index 70.88
Plus_FRiP 0.4
Minus_FRiP 0.37
mRNA_contamination 1.16
Time 3:27:15
Success 02-27-12:53:18

H9_treated_PRO-seq_2 objects

Links
Figures
Fig.0 Adapter insertion distribution
Fig.1 Library complexity
Fig.2 TSS enrichment
Fig.3 Pause index
Fig.4 cFRiF
Fig.5 FRiF
Fig.6 mRNA contamination